#!/usr/bin/perl
#
# Copyright (c) 2013 Luciano Xumerle. All rights reserved.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2
# as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; see the file COPYING.  If not, write to the Free
# Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
#

use strict;
use warnings;

open( FILE, $ARGV[0] ) || die "INPUT MUST BE A FASTA FILE!!!\n\n";
my $chrom = '';
my $line  = '';
while (<FILE>)
{
    chomp;
    if (m/^>(.+)\s+.+$/)
    {
        if ( $chrom ne $line )
        {
            &printFile( $chrom, $line );
        }
        $chrom = $1;
        $line  = '';
    }
    else
    {
        $line .= $_;
    }
}
&printFile( $chrom, $line );

close FILE;

sub printFile
{
    my $chrom = shift;
    my $line  = shift;
    $chrom =~ s/\s+.+$//;
    open( RES, ">$chrom" . '.bin' ) || die;
    print RES $line;
    close RES;
}
